pin h5py version, avoid environment before/after build

pin h5py, don't use environment_after.yml
OpenChemistry · Apr 14, 2023 · b36cebc · b36cebc
1 parent 1cc8150
commit b36cebc
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Showing 12 changed files with 56 additions and 41 deletions.
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - "master"
+      - "update-dockerfile-staging"
   pull_request:
     branches:
       - "master"
@@ -23,6 +24,18 @@ jobs:
             tag-suffix: -conda-jammy
 
     steps:
+
+      - 
+        name: Sets DOCKERHUB_ORG if pushing to fork
+        run: |
+          echo "DOCKERHUB_ORG=${{ vars.DOCKERHUB_ORG }}" >> $GITHUB_ENV
+        if: ${{ github.event_name != 'pull_request' }}
+
+      - 
+        name: Sets DOCKERHUB_ORG if  PR
+        run: |
+          echo "DOCKERHUB_ORG=openchemistry" >> $GITHUB_ENV
+        if: ${{ github.event_name == 'pull_request' }}
       -
         name: Checkout
         uses: actions/checkout@v3
@@ -56,10 +69,11 @@ jobs:
           push: ${{ github.event_name != 'pull_request' }}
           build-args: | 
                       DOCKERFILE_SUBDIR=${{ matrix.version }}${{ matrix.tag-suffix}}
-          tags: ${{ vars.DOCKERHUB_ORG }}/${{ matrix.version }}-base:latest${{ matrix.tag-suffix }}
+          tags: ${{ env.DOCKERHUB_ORG }}/${{ matrix.version }}-base:latest${{ matrix.tag-suffix }}
           cache-to: type=gha
           cache-from: type=gha,mode=max
 
+
 # Builds stempy every time after build-base is done
   build-stempy:
     runs-on: ubuntu-latest
@@ -85,9 +99,21 @@ jobs:
         with:
           fetch-depth: 0
           submodules: 'recursive'
+      - 
+        name: Sets DOCKERHUB_ORG if pushing to fork
+        run: |
+          echo "DOCKERHUB_ORG=${{ vars.DOCKERHUB_ORG }}" >> $GITHUB_ENV
+        if: ${{ github.event_name != 'pull_request' }}
+
+      - 
+        name: Sets DOCKERHUB_ORG if  PR
+        run: |
+          echo "DOCKERHUB_ORG=openchemistry" >> $GITHUB_ENV
+        if: ${{ github.event_name == 'pull_request' }}
       -
         name: Login to Docker Hub
         uses: docker/login-action@v2
+        if: ${{ github.event_name != 'pull_request' }}
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -102,9 +128,9 @@ jobs:
           file: ./docker/${{ matrix.version }}${{ matrix.tag-suffix}}/Dockerfile.stempy${{matrix.notebook}}
           build-args: | 
                       DOCKERFILE_SUBDIR=${{ matrix.version }}${{ matrix.tag-suffix}}
-                      DOCKERHUB_ORG=${{ vars.DOCKERHUB_ORG }}
+                      DOCKERHUB_ORG=${{ env.DOCKERHUB_ORG }}
           push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ vars.DOCKERHUB_ORG }}/${{ matrix.version }}${{matrix.notebook}}:latest${{ matrix.tag-suffix}}
+          tags: ${{ env.DOCKERHUB_ORG }}/${{ matrix.version }}${{matrix.notebook}}:latest${{ matrix.tag-suffix}}
 
   # Seperate job for building original version
   build-stempy-old:
@@ -123,9 +149,21 @@ jobs:
         with:
           fetch-depth: 0
           submodules: 'recursive'
+      - 
+        name: Sets DOCKERHUB_ORG if pushing to fork
+        run: |
+          echo "DOCKERHUB_ORG=${{ vars.DOCKERHUB_ORG }}" >> $GITHUB_ENV
+        if: ${{ github.event_name != 'pull_request' }}
+
+      - 
+        name: Sets DOCKERHUB_ORG if  PR
+        run: |
+          echo "DOCKERHUB_ORG=openchemistry" >> $GITHUB_ENV
+        if: ${{ github.event_name == 'pull_request' }}
       -
         name: Login to Docker Hub
         uses: docker/login-action@v2
+        if: ${{ github.event_name != 'pull_request' }}
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -140,7 +178,7 @@ jobs:
           context: .
           file: ./docker/Dockerfile
           push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ vars.DOCKERHUB_ORG }}/${{ matrix.version }}:latest
+          tags: ${{ env.DOCKERHUB_ORG }}/${{ matrix.version }}:latest
           build-args: |
                       MPI=${{ matrix.MPI }}
           cache-to: type=gha
@@ -154,4 +192,4 @@ jobs:
           context: .
           file: ./docker/Dockerfile.ipykernel
           push: ${{ github.event_name != 'pull_request' }}
-          tags: ${{ vars.DOCKERHUB_ORG }}/${{ matrix.version }}-ipykernel:latest
+          tags: ${{ env.DOCKERHUB_ORG }}/${{ matrix.version }}-ipykernel:latest
diff --git a/docker/stempy-conda-jammy/Dockerfile.stempy b/docker/stempy-conda-jammy/Dockerfile.stempy
@@ -8,7 +8,7 @@ WORKDIR /source
 COPY . /source/stempy/
 ARG CONDA_ENV_DIR=/source/stempy/docker/${DOCKERFILE_SUBDIR}/conda
 
-RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml                     && \
+RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment.yml                     && \
   mkdir -p /build/stempy                                                                    && \
   cd /build/stempy                                                                          && \
   cmake -DCMAKE_BUILD_TYPE:STRING=Release \
@@ -18,7 +18,6 @@ RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml
   make -j 16                                                                                && \
   cp -r -L /build/stempy/lib/stempy \                                                   
   /opt/miniconda3/lib/python${PYTHON_VERSION}/site-packages                                 && \
-  mamba env update -n base -f ${CONDA_ENV_DIR}/environment_after.yml                        && \
   rm -rf /source/stempy                                                                     && \
   conda clean -a -y -q
 

diff --git a/docker/stempy-conda-jammy/Dockerfile.stempy-ipykernel b/docker/stempy-conda-jammy/Dockerfile.stempy-ipykernel
@@ -8,7 +8,7 @@ WORKDIR /source
 COPY . /source/stempy/
 ARG CONDA_ENV_DIR=/source/stempy/docker/${DOCKERFILE_SUBDIR}/conda
 
-RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml                     && \
+RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_ipykernel.yml                  && \
   mkdir -p /build/stempy                                                                    && \
   cd /build/stempy                                                                          && \
   cmake -DCMAKE_BUILD_TYPE:STRING=Release \
@@ -18,7 +18,6 @@ RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml
   make -j 16                                                                                && \
   cp -r -L /build/stempy/lib/stempy \                                                   
   /opt/miniconda3/lib/python${PYTHON_VERSION}/site-packages                                 && \
-  mamba env update -n base -f ${CONDA_ENV_DIR}/environment_ipykernel.yml                    && \
   rm -rf /source/stempy                                                                     && \
   conda clean -a -y -q
 

diff --git a/...y-conda-jammy/conda/environment_after.yml → .../stempy-conda-jammy/conda/environment.yml b/...y-conda-jammy/conda/environment_after.yml → .../stempy-conda-jammy/conda/environment.yml
@@ -8,4 +8,6 @@ dependencies:
   - click 
   - imageio 
   - ncempy
-  - h5py=3.6
+  - h5py=3.6
+  - pip:
+    - cmake
diff --git a/docker/stempy-conda-jammy/conda/environment_before.yml b/docker/stempy-conda-jammy/conda/environment_before.yml
diff --git a/docker/stempy-conda-jammy/conda/environment_ipykernel.yml b/docker/stempy-conda-jammy/conda/environment_ipykernel.yml
@@ -11,4 +11,6 @@ dependencies:
   - h5py=3.6
   - ipykernel=6.4.2
   - ipympl=0.8.6
-  - matplotlib=3.4.3
+  - matplotlib=3.4.3
+  - pip:
+    - cmake
diff --git a/docker/stempy-mpi-conda-jammy/Dockerfile.stempy b/docker/stempy-mpi-conda-jammy/Dockerfile.stempy
@@ -8,7 +8,7 @@ WORKDIR /source
 COPY . /source/stempy/
 ARG CONDA_ENV_DIR=/source/stempy/docker/${DOCKERFILE_SUBDIR}/conda
 
-RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml                     && \
+RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment.yml                            && \
   mkdir -p /build/stempy                                                                    && \
   cd /build/stempy                                                                          && \
   cmake -DCMAKE_BUILD_TYPE:STRING=Release \
@@ -18,10 +18,7 @@ RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml
   make -j 16                                                                                && \
   cp -r -L /build/stempy/lib/stempy \
   /opt/miniconda3/lib/python${PYTHON_VERSION}/site-packages                                 && \
-  mamba env update -n base -f ${CONDA_ENV_DIR}/environment_after.yml                        && \
   rm -rf /source/stempy                                                                     && \
   conda clean -a -y -q
 
-RUN /sbin/ldconfig
-
-
+RUN /sbin/ldconfig
diff --git a/...i-conda-jammy/conda/environment_after.yml → ...mpy-mpi-conda-jammy/conda/environment.yml b/...i-conda-jammy/conda/environment_after.yml → ...mpy-mpi-conda-jammy/conda/environment.yml
@@ -10,4 +10,5 @@ dependencies:
   - ncempy
   - h5py=2.10
   - pip:
+    - cmake
     - mpi4py==3.1.4
diff --git a/docker/stempy-mpi-conda-jammy/conda/environment_before.yml b/docker/stempy-mpi-conda-jammy/conda/environment_before.yml
diff --git a/docker/stempy-mpi-conda/Dockerfile.stempy b/docker/stempy-mpi-conda/Dockerfile.stempy
@@ -8,7 +8,7 @@ WORKDIR /source
 COPY . /source/stempy/
 ARG CONDA_ENV_DIR=/source/stempy/docker/${DOCKERFILE_SUBDIR}/conda
 
-RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml                   && \
+RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment.yml                          && \
   mkdir -p /build/stempy                                                                  && \
   cd /build/stempy                                                                        && \
   cmake -DCMAKE_BUILD_TYPE:STRING=Release \
@@ -18,7 +18,6 @@ RUN mamba env update -n base -f ${CONDA_ENV_DIR}/environment_before.yml
   make -j 16                                                                              && \
   cp -r -L /build/stempy/lib/stempy \
   /opt/miniconda3/lib/python${PYTHON_VERSION}/site-packages                               && \
-  mamba env update -n base -f ${CONDA_ENV_DIR}/environment_after.yml                      && \
   rm -rf /source/stempy                                                                   && \
   conda clean -a -y -q
 

diff --git a/...mpy-mpi-conda/conda/environment_after.yml → ...er/stempy-mpi-conda/conda/environment.yml b/...mpy-mpi-conda/conda/environment_after.yml → ...er/stempy-mpi-conda/conda/environment.yml
@@ -10,4 +10,5 @@ dependencies:
   - ncempy
   - h5py=2.10
   - pip:
+    - cmake
     - mpi4py==3.1.4
diff --git a/docker/stempy-mpi-conda/conda/environment_before.yml b/docker/stempy-mpi-conda/conda/environment_before.yml
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,4 +8,6 @@ dependencies: @@
       - click
       - imageio
       - ncempy
-      - h5py=3.6
+      - h5py=3.6
+      - pip:
+        - cmake